Format

Send to:

Choose Destination
    • Showing Current items.

    PRDM9 PR/SET domain 9 [ Homo sapiens (human) ]

    Gene ID: 56979, updated on 17-Jun-2019

    Summary

    Official Symbol
    PRDM9provided by HGNC
    Official Full Name
    PR/SET domain 9provided by HGNC
    Primary source
    HGNC:HGNC:13994
    See related
    Ensembl:ENSG00000164256 MIM:609760
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PFM6; KMT8B; MSBP3; ZNF899; MEISETZ
    Summary
    The protein encoded by this gene is a zinc finger protein with histone methyltransferase activity that catalyzes histone H3 lysine 4 trimethylation (H3K4me3) during meiotic prophase. This protein contains multiple domains, including a Kruppel-associated box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and RIZ homologous region, a subclass of SET (PR/SET) domain, and a tandem array of C2H2 zinc fingers. The zinc finger array recognizes a short sequence motif, leading to local H3K4me3, and meiotic recombination hotspot activity. The observed allelic variation alters the DNA-binding sequence specificity of the protein, resulting in distinct meiotic recombination hotspots amongst individuals and populations. Multiple alternate alleles of this gene have been described. [provided by RefSeq, Jul 2015]
    Expression
    Restricted expression toward testis (RPKM 2.2) See more
    Orthologs

    Genomic context

    See PRDM9 in Genome Data Viewer
    Location:
    5p14.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (23507609..23528597)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (23507724..23528706)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase non-receptor type 11 pseudogene Neighboring gene uncharacterized LOC105374688 Neighboring gene uncharacterized LOC107986377 Neighboring gene chromosome 5 open reading frame 17 (putative) Neighboring gene AKT interacting protein pseudogene Neighboring gene AKT interacting protein pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Fine-scale recombination rate differences between sexes, populations and individuals.
    NHGRI GWA Catalog
    The landscape of recombination in African Americans.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Cell Cycle, organism-specific biosystem (from REACTOME)
      Cell Cycle, organism-specific biosystem
      Cell Cycle
    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • Lysine degradation, organism-specific biosystem (from KEGG)
      Lysine degradation, organism-specific biosystem
      Lysine degradation
    • Lysine degradation, conserved biosystem (from KEGG)
      Lysine degradation, conserved biosystem
      Lysine degradation
    • Meiosis, organism-specific biosystem (from REACTOME)
      Meiosis, organism-specific biosystemDuring meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing...
    • Meiotic recombination, organism-specific biosystem (from REACTOME)
      Meiotic recombination, organism-specific biosystemMeiotic recombination exchanges segments of duplex DNA between chromosomal homologs, generating genetic diversity (reviewed in Handel and Schimenti 2010, Inagaki et al. 2010, Cohen et al. 2006). Ther...
    • PKMTs methylate histone lysines, organism-specific biosystem (from REACTOME)
      PKMTs methylate histone lysines, organism-specific biosystemLysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM),...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    RNA polymerase II regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    histone methyltransferase activity (H3-K4 specific) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    histone-lysine N-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    recombination hotspot binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription regulatory region DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    histone H3-K4 methylation IEA
    Inferred from Electronic Annotation
    more info
     
    meiotic gene conversion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleosome positioning IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of reciprocal meiotic recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of reciprocal meiotic recombination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase PRDM9
    Names
    PR domain 9
    PR domain containing 9
    PR domain zinc finger protein 9
    histone methyl transferase
    minisatellite binding protein 3 (115kD)
    NP_064612.2

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001310214.1NP_001297143.1  histone-lysine N-methyltransferase PRDM9 isoform PRDM9 A

      See identical proteins and their annotated locations for NP_001297143.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PRDM9 A allele, PMID:20044539) differs in the 5' and 3' UTRs, and contains a single nucleotide difference in the CDS, compared to the PRDM9 B allele. It encodes PRDM9 A, an isoform with a serine at amino acid 681, rather than the threonine found at this position in the PRDM9 B isoform.
      Source sequence(s)
      AK301776
      UniProtKB/Swiss-Prot
      Q9NQV7
      Conserved Domains (7) summary
      smart00317
      Location:246364
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00349
      Location:2785
      KRAB; krueppel associated box
      COG5048
      Location:611878
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:750770
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:2762
      KRAB; KRAB box
      pfam09514
      Location:171201
      SSXRD; SSXRD motif
      pfam13465
      Location:846870
      zf-H2C2_2; Zinc-finger double domain
    2. NM_020227.3NP_064612.2  histone-lysine N-methyltransferase PRDM9 isoform PRDM9 B

      See identical proteins and their annotated locations for NP_064612.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (PRDM9 B allele, PMID:20044539) matches the reference genome sequence and encodes isoform PRDM9 B.
      Source sequence(s)
      AC025451, DB636359, DQ388610
      Consensus CDS
      CCDS43307.1
      UniProtKB/Swiss-Prot
      Q9NQV7
      Related
      ENSP00000296682.3, ENST00000296682.3
      Conserved Domains (7) summary
      smart00317
      Location:246364
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00349
      Location:2785
      KRAB; krueppel associated box
      COG5048
      Location:611878
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:750770
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:2762
      KRAB; KRAB box
      pfam09514
      Location:171201
      SSXRD; SSXRD motif
      pfam13465
      Location:846870
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      23507609..23528597
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center